Hi,
I'm having trouble compiling Sage on a CentOS linux machine.
The problem seems to be in compiling matplotlib and R.
I'm attaching the log files here.
matplotlib seems to complain that I need to install freetype-devel and
pkg-config with yum but I did that and yum returns
"Package freetype-devel-2.3.11-17.el6.x86_64 already installed and latest
version"
"Package 1:pkgconfig-0.23-9.1.el6.x86_64 already installed and latest
version"
while R is complaining that something about zlib isn't available. So again
I installed zlib and zlib-devel with yum
and both were already installed.
I'm attaching the log files for matplotlib and R.
Any help is greatly appreciated.
Thanks,
-Mike
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Found local metadata for matplotlib-2.2.4.p0
Using cached file /usr/local/sage-8.9/upstream/matplotlib-2.2.4.tar.bz2
matplotlib-2.2.4.p0
====================================================
Setting up build directory for matplotlib-2.2.4.p0
Finished extraction
Applying patches from ../patches...
Applying ../patches/install-jquery-ui.patch
patching file setupext.py
Applying ../patches/python38.patch
patching file setup.py
Applying ../patches/setup.py.patch
patching file setup.py
Hunk #1 succeeded at 67 (offset -18 lines).
****************************************************
Host system:
Linux algebra.math.yorku.ca 2.6.32-754.23.1.el6.centos.plus.x86_64 #1 SMP Thu
Sep 26 11:58:20 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/sage-8.9/local/libexec/gcc/x86_64-pc-linux-gnu/7.4.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: ../src/configure --prefix=/usr/local/sage-8.9/local
--with-local-prefix=/usr/local/sage-8.9/local
--with-gmp=/usr/local/sage-8.9/local --with-mpfr=/usr/local/sage-8.9/local
--with-mpc=/usr/local/sage-8.9/local --with-system-zlib --without-isl
--disable-multilib --disable-nls --disable-libitm
--enable-languages=c,c++,fortran
Thread model: posix
gcc version 7.4.0 (GCC)
****************************************************
Package 'matplotlib' is currently not installed
No legacy uninstaller found for 'matplotlib'; nothing to do
NOTE: Set SAGE_MATPLOTLIB_GUI to anything but 'no' to try to build the
Matplotlib GUI.
Not building any matplotlib graphical backends.
Installing matplotlib-2.2.4.p0
Installing package matplotlib using pip2
Ignoring indexes: https://pypi.org/simple
Created temporary directory: /tmp/pip-ephem-wheel-cache-gAKo5J
Created temporary directory: /tmp/pip-req-tracker-VPLkhj
Created requirements tracker '/tmp/pip-req-tracker-VPLkhj'
Created temporary directory: /tmp/pip-install-zhwCLb
Processing /usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src
Created temporary directory: /tmp/pip-req-build-vCShvr
Added
file:///usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src to
build tracker '/tmp/pip-req-tracker-VPLkhj'
Running setup.py (path:/tmp/pip-req-build-vCShvr/setup.py) egg_info for
package from
file:///usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src
Running command python setup.py egg_info
============================================================================
Edit setup.cfg to change the build options
BUILDING MATPLOTLIB
matplotlib: yes [2.2.4]
python: yes [2.7.15 (default, Nov 12 2019, 03:11:15) [GCC
7.4.0]]
platform: yes [linux2]
REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.16.1]
install_requires: yes [handled by setuptools]
libagg: yes [pkg-config information for 'libagg' could not
be found. Using local copy.]
freetype: no [The C/C++ header for freetype2 (ft2build.h)
could not be found. You may need to install the
development package.]
png: yes [version 1.2.49]
qhull: yes [pkg-config information for 'libqhull' could not
be found. Using local copy.]
OPTIONAL SUBPACKAGES
sample_data: yes [installing]
toolkits: yes [installing]
OPTIONAL BACKEND EXTENSIONS
macosx: no [skipping due to configuration]
qt5agg: no [PySide2 not found; PyQt5 not found]
qt4agg: no [PySide not found; PyQt4 not found]
gtk3agg: no [Requires pygobject to be installed.]
gtk3cairo: no [Requires cairocffi or pycairo to be installed.]
gtkagg: no [skipping due to configuration]
tkagg: yes [installing; run-time loading from Python Tcl /
Tk]
wxagg: no [skipping due to configuration]
gtk: no [skipping due to configuration]
agg: yes [installing]
cairo: no [cairocffi or pycairo not found]
windowing: no [skipping due to configuration]
OPTIONAL LATEX DEPENDENCIES
dvipng: yes [version 1.11]
ghostscript: yes [version 8.70]
latex: yes [version 3.141592]
pdftops: no
OPTIONAL PACKAGE DATA
dlls: no [skipping due to configuration]
============================================================================
* The following required packages can not be built:
* freetype
* Try installing freetype with `yum install
* freetype-devel` and pkg-config with `yum install
* pkg-config`
Cleaning up...
Removing source in /tmp/pip-req-build-vCShvr
Removed
file:///usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src
from build tracker '/tmp/pip-req-tracker-VPLkhj'
Removed build tracker '/tmp/pip-req-tracker-VPLkhj'
Command "python setup.py egg_info" failed with error code 1 in
/tmp/pip-req-build-vCShvr/
Exception information:
Traceback (most recent call last):
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/cli/base_command.py",
line 143, in main
status = self.run(options, args)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/commands/install.py",
line 318, in run
resolver.resolve(requirement_set)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
line 102, in resolve
self._resolve_one(requirement_set, req)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
line 256, in _resolve_one
abstract_dist = self._get_abstract_dist_for(req_to_install)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
line 209, in _get_abstract_dist_for
self.require_hashes
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/operations/prepare.py",
line 298, in prepare_linked_requirement
abstract_dist.prep_for_dist(finder, self.build_isolation)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/operations/prepare.py",
line 126, in prep_for_dist
self.req.run_egg_info()
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/req/req_install.py",
line 473, in run_egg_info
command_desc='python setup.py egg_info')
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/utils/misc.py",
line 705, in call_subprocess
% (command_desc, proc.returncode, cwd))
InstallationError: Command "python setup.py egg_info" failed with error code 1
in /tmp/pip-req-build-vCShvr/
Error: installing with pip2 failed
********************************************************************************
Error installing matplotlib-2.2.4.p0
********************************************************************************
real 0m3.674s
user 0m2.204s
sys 0m1.210s
************************************************************************
Error installing package matplotlib-2.2.4.p0
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the log file
/usr/local/sage-8.9/logs/pkgs/matplotlib-2.2.4.p0.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0 and type
'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0' &&
'/usr/local/sage-8.9/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
Found local metadata for matplotlib-2.2.4.p0
Using cached file /usr/local/sage-8.9/upstream/matplotlib-2.2.4.tar.bz2
matplotlib-2.2.4.p0
====================================================
Setting up build directory for matplotlib-2.2.4.p0
Finished extraction
Applying patches from ../patches...
Applying ../patches/install-jquery-ui.patch
patching file setupext.py
Applying ../patches/python38.patch
patching file setup.py
Applying ../patches/setup.py.patch
patching file setup.py
Hunk #1 succeeded at 67 (offset -18 lines).
****************************************************
Host system:
Linux algebra.math.yorku.ca 2.6.32-754.23.1.el6.centos.plus.x86_64 #1 SMP Thu
Sep 26 11:58:20 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/sage-8.9/local/libexec/gcc/x86_64-pc-linux-gnu/7.4.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: ../src/configure --prefix=/usr/local/sage-8.9/local
--with-local-prefix=/usr/local/sage-8.9/local
--with-gmp=/usr/local/sage-8.9/local --with-mpfr=/usr/local/sage-8.9/local
--with-mpc=/usr/local/sage-8.9/local --with-system-zlib --without-isl
--disable-multilib --disable-nls --disable-libitm
--enable-languages=c,c++,fortran
Thread model: posix
gcc version 7.4.0 (GCC)
****************************************************
Package 'matplotlib' is currently not installed
No legacy uninstaller found for 'matplotlib'; nothing to do
NOTE: Set SAGE_MATPLOTLIB_GUI to anything but 'no' to try to build the
Matplotlib GUI.
Not building any matplotlib graphical backends.
Installing matplotlib-2.2.4.p0
Installing package matplotlib using pip2
Ignoring indexes: https://pypi.org/simple
Created temporary directory: /tmp/pip-ephem-wheel-cache-50JgyC
Created temporary directory: /tmp/pip-req-tracker-h3dafz
Created requirements tracker '/tmp/pip-req-tracker-h3dafz'
Created temporary directory: /tmp/pip-install-J1GWyp
Processing /usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src
Created temporary directory: /tmp/pip-req-build-zGO7ez
Added
file:///usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src to
build tracker '/tmp/pip-req-tracker-h3dafz'
Running setup.py (path:/tmp/pip-req-build-zGO7ez/setup.py) egg_info for
package from
file:///usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src
Running command python setup.py egg_info
============================================================================
Edit setup.cfg to change the build options
BUILDING MATPLOTLIB
matplotlib: yes [2.2.4]
python: yes [2.7.15 (default, Nov 12 2019, 03:11:15) [GCC
7.4.0]]
platform: yes [linux2]
REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.16.1]
install_requires: yes [handled by setuptools]
libagg: yes [pkg-config information for 'libagg' could not
be found. Using local copy.]
freetype: no [The C/C++ header for freetype2 (ft2build.h)
could not be found. You may need to install the
development package.]
png: yes [version 1.2.49]
qhull: yes [pkg-config information for 'libqhull' could not
be found. Using local copy.]
OPTIONAL SUBPACKAGES
sample_data: yes [installing]
toolkits: yes [installing]
OPTIONAL BACKEND EXTENSIONS
macosx: no [skipping due to configuration]
qt5agg: no [PySide2 not found; PyQt5 not found]
qt4agg: no [PySide not found; PyQt4 not found]
gtk3agg: no [Requires pygobject to be installed.]
gtk3cairo: no [Requires cairocffi or pycairo to be installed.]
gtkagg: no [skipping due to configuration]
tkagg: yes [installing; run-time loading from Python Tcl /
Tk]
wxagg: no [skipping due to configuration]
gtk: no [skipping due to configuration]
agg: yes [installing]
cairo: no [cairocffi or pycairo not found]
windowing: no [skipping due to configuration]
OPTIONAL LATEX DEPENDENCIES
dvipng: yes [version 1.11]
ghostscript: yes [version 8.70]
latex: yes [version 3.141592]
pdftops: no
OPTIONAL PACKAGE DATA
dlls: no [skipping due to configuration]
============================================================================
* The following required packages can not be built:
* freetype
* Try installing freetype with `yum install
* freetype-devel` and pkg-config with `yum install
* pkg-config`
Cleaning up...
Removing source in /tmp/pip-req-build-zGO7ez
Removed
file:///usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src
from build tracker '/tmp/pip-req-tracker-h3dafz'
Removed build tracker '/tmp/pip-req-tracker-h3dafz'
Command "python setup.py egg_info" failed with error code 1 in
/tmp/pip-req-build-zGO7ez/
Exception information:
Traceback (most recent call last):
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/cli/base_command.py",
line 143, in main
status = self.run(options, args)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/commands/install.py",
line 318, in run
resolver.resolve(requirement_set)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
line 102, in resolve
self._resolve_one(requirement_set, req)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
line 256, in _resolve_one
abstract_dist = self._get_abstract_dist_for(req_to_install)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
line 209, in _get_abstract_dist_for
self.require_hashes
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/operations/prepare.py",
line 298, in prepare_linked_requirement
abstract_dist.prep_for_dist(finder, self.build_isolation)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/operations/prepare.py",
line 126, in prep_for_dist
self.req.run_egg_info()
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/req/req_install.py",
line 473, in run_egg_info
command_desc='python setup.py egg_info')
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/utils/misc.py",
line 705, in call_subprocess
% (command_desc, proc.returncode, cwd))
InstallationError: Command "python setup.py egg_info" failed with error code 1
in /tmp/pip-req-build-zGO7ez/
Error: installing with pip2 failed
********************************************************************************
Error installing matplotlib-2.2.4.p0
********************************************************************************
real 0m4.988s
user 0m2.271s
sys 0m1.292s
************************************************************************
Error installing package matplotlib-2.2.4.p0
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the log file
/usr/local/sage-8.9/logs/pkgs/matplotlib-2.2.4.p0.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0 and type
'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0' &&
'/usr/local/sage-8.9/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
Found local metadata for matplotlib-2.2.4.p0
Using cached file /usr/local/sage-8.9/upstream/matplotlib-2.2.4.tar.bz2
matplotlib-2.2.4.p0
====================================================
Setting up build directory for matplotlib-2.2.4.p0
Finished extraction
Applying patches from ../patches...
Applying ../patches/install-jquery-ui.patch
patching file setupext.py
Applying ../patches/python38.patch
patching file setup.py
Applying ../patches/setup.py.patch
patching file setup.py
Hunk #1 succeeded at 67 (offset -18 lines).
****************************************************
Host system:
Linux algebra.math.yorku.ca 2.6.32-754.23.1.el6.centos.plus.x86_64 #1 SMP Thu
Sep 26 11:58:20 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/sage-8.9/local/libexec/gcc/x86_64-pc-linux-gnu/7.4.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: ../src/configure --prefix=/usr/local/sage-8.9/local
--with-local-prefix=/usr/local/sage-8.9/local
--with-gmp=/usr/local/sage-8.9/local --with-mpfr=/usr/local/sage-8.9/local
--with-mpc=/usr/local/sage-8.9/local --with-system-zlib --without-isl
--disable-multilib --disable-nls --disable-libitm
--enable-languages=c,c++,fortran
Thread model: posix
gcc version 7.4.0 (GCC)
****************************************************
Package 'matplotlib' is currently not installed
No legacy uninstaller found for 'matplotlib'; nothing to do
NOTE: Set SAGE_MATPLOTLIB_GUI to anything but 'no' to try to build the
Matplotlib GUI.
Not building any matplotlib graphical backends.
Installing matplotlib-2.2.4.p0
Installing package matplotlib using pip2
Waiting for shared lock to run /usr/local/sage-8.9/local/bin/python2 -m pip
install --ignore-installed --verbose --no-deps --no-index --isolated
--no-build-isolation
--root=/usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/inst .
... ok
Ignoring indexes: https://pypi.org/simple
Created temporary directory: /tmp/pip-ephem-wheel-cache-5pzn0d
Created temporary directory: /tmp/pip-req-tracker-LL7VRi
Created requirements tracker '/tmp/pip-req-tracker-LL7VRi'
Created temporary directory: /tmp/pip-install-gw_bZw
Processing /usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src
Created temporary directory: /tmp/pip-req-build-ZNxMTI
Added
file:///usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src to
build tracker '/tmp/pip-req-tracker-LL7VRi'
Running setup.py (path:/tmp/pip-req-build-ZNxMTI/setup.py) egg_info for
package from
file:///usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src
Running command python setup.py egg_info
============================================================================
Edit setup.cfg to change the build options
BUILDING MATPLOTLIB
matplotlib: yes [2.2.4]
python: yes [2.7.15 (default, Nov 12 2019, 03:11:15) [GCC
7.4.0]]
platform: yes [linux2]
REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.16.1]
install_requires: yes [handled by setuptools]
libagg: yes [pkg-config information for 'libagg' could not
be found. Using local copy.]
freetype: no [The C/C++ header for freetype2 (ft2build.h)
could not be found. You may need to install the
development package.]
png: yes [version 1.2.49]
qhull: yes [pkg-config information for 'libqhull' could not
be found. Using local copy.]
OPTIONAL SUBPACKAGES
sample_data: yes [installing]
toolkits: yes [installing]
OPTIONAL BACKEND EXTENSIONS
macosx: no [skipping due to configuration]
qt5agg: no [PySide2 not found; PyQt5 not found]
qt4agg: no [PySide not found; PyQt4 not found]
gtk3agg: no [Requires pygobject to be installed.]
gtk3cairo: no [Requires cairocffi or pycairo to be installed.]
gtkagg: no [skipping due to configuration]
tkagg: yes [installing; run-time loading from Python Tcl /
Tk]
wxagg: no [skipping due to configuration]
gtk: no [skipping due to configuration]
agg: yes [installing]
cairo: no [cairocffi or pycairo not found]
windowing: no [skipping due to configuration]
OPTIONAL LATEX DEPENDENCIES
dvipng: yes [version 1.11]
ghostscript: yes [version 8.70]
latex: yes [version 3.141592]
pdftops: no
OPTIONAL PACKAGE DATA
dlls: no [skipping due to configuration]
============================================================================
* The following required packages can not be built:
* freetype
* Try installing freetype with `yum install
* freetype-devel` and pkg-config with `yum install
* pkg-config`
Cleaning up...
Removing source in /tmp/pip-req-build-ZNxMTI
Removed
file:///usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src
from build tracker '/tmp/pip-req-tracker-LL7VRi'
Removed build tracker '/tmp/pip-req-tracker-LL7VRi'
Command "python setup.py egg_info" failed with error code 1 in
/tmp/pip-req-build-ZNxMTI/
Exception information:
Traceback (most recent call last):
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/cli/base_command.py",
line 143, in main
status = self.run(options, args)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/commands/install.py",
line 318, in run
resolver.resolve(requirement_set)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
line 102, in resolve
self._resolve_one(requirement_set, req)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
line 256, in _resolve_one
abstract_dist = self._get_abstract_dist_for(req_to_install)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
line 209, in _get_abstract_dist_for
self.require_hashes
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/operations/prepare.py",
line 298, in prepare_linked_requirement
abstract_dist.prep_for_dist(finder, self.build_isolation)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/operations/prepare.py",
line 126, in prep_for_dist
self.req.run_egg_info()
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/req/req_install.py",
line 473, in run_egg_info
command_desc='python setup.py egg_info')
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/utils/misc.py",
line 705, in call_subprocess
% (command_desc, proc.returncode, cwd))
InstallationError: Command "python setup.py egg_info" failed with error code 1
in /tmp/pip-req-build-ZNxMTI/
Error: installing with pip2 failed
********************************************************************************
Error installing matplotlib-2.2.4.p0
********************************************************************************
real 2m23.573s
user 0m2.340s
sys 0m1.305s
************************************************************************
Error installing package matplotlib-2.2.4.p0
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the log file
/usr/local/sage-8.9/logs/pkgs/matplotlib-2.2.4.p0.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0 and type
'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0' &&
'/usr/local/sage-8.9/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
Found local metadata for matplotlib-2.2.4.p0
Using cached file /usr/local/sage-8.9/upstream/matplotlib-2.2.4.tar.bz2
matplotlib-2.2.4.p0
====================================================
Setting up build directory for matplotlib-2.2.4.p0
Finished extraction
Applying patches from ../patches...
Applying ../patches/install-jquery-ui.patch
patching file setupext.py
Applying ../patches/python38.patch
patching file setup.py
Applying ../patches/setup.py.patch
patching file setup.py
Hunk #1 succeeded at 67 (offset -18 lines).
****************************************************
Host system:
Linux algebra.math.yorku.ca 2.6.32-754.23.1.el6.centos.plus.x86_64 #1 SMP Thu
Sep 26 11:58:20 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/sage-8.9/local/libexec/gcc/x86_64-pc-linux-gnu/7.4.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: ../src/configure --prefix=/usr/local/sage-8.9/local
--with-local-prefix=/usr/local/sage-8.9/local
--with-gmp=/usr/local/sage-8.9/local --with-mpfr=/usr/local/sage-8.9/local
--with-mpc=/usr/local/sage-8.9/local --with-system-zlib --without-isl
--disable-multilib --disable-nls --disable-libitm
--enable-languages=c,c++,fortran
Thread model: posix
gcc version 7.4.0 (GCC)
****************************************************
Package 'matplotlib' is currently not installed
No legacy uninstaller found for 'matplotlib'; nothing to do
NOTE: Set SAGE_MATPLOTLIB_GUI to anything but 'no' to try to build the
Matplotlib GUI.
Not building any matplotlib graphical backends.
Installing matplotlib-2.2.4.p0
Installing package matplotlib using pip2
Ignoring indexes: https://pypi.org/simple
Created temporary directory: /tmp/pip-ephem-wheel-cache-HUSLU5
Created temporary directory: /tmp/pip-req-tracker-EMXWiP
Created requirements tracker '/tmp/pip-req-tracker-EMXWiP'
Created temporary directory: /tmp/pip-install-LngeSm
Processing /usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src
Created temporary directory: /tmp/pip-req-build-qhS9W4
Added
file:///usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src to
build tracker '/tmp/pip-req-tracker-EMXWiP'
Running setup.py (path:/tmp/pip-req-build-qhS9W4/setup.py) egg_info for
package from
file:///usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src
Running command python setup.py egg_info
============================================================================
Edit setup.cfg to change the build options
BUILDING MATPLOTLIB
matplotlib: yes [2.2.4]
python: yes [2.7.15 (default, Nov 12 2019, 03:11:15) [GCC
7.4.0]]
platform: yes [linux2]
REQUIRED DEPENDENCIES AND EXTENSIONS
numpy: yes [version 1.16.1]
install_requires: yes [handled by setuptools]
libagg: yes [pkg-config information for 'libagg' could not
be found. Using local copy.]
freetype: no [The C/C++ header for freetype2 (ft2build.h)
could not be found. You may need to install the
development package.]
png: yes [version 1.2.49]
qhull: yes [pkg-config information for 'libqhull' could not
be found. Using local copy.]
OPTIONAL SUBPACKAGES
sample_data: yes [installing]
toolkits: yes [installing]
OPTIONAL BACKEND EXTENSIONS
macosx: no [skipping due to configuration]
qt5agg: no [PySide2 not found; PyQt5 not found]
qt4agg: no [PySide not found; PyQt4 not found]
gtk3agg: no [Requires pygobject to be installed.]
gtk3cairo: no [Requires cairocffi or pycairo to be installed.]
gtkagg: no [skipping due to configuration]
tkagg: yes [installing; run-time loading from Python Tcl /
Tk]
wxagg: no [skipping due to configuration]
gtk: no [skipping due to configuration]
agg: yes [installing]
cairo: no [cairocffi or pycairo not found]
windowing: no [skipping due to configuration]
OPTIONAL LATEX DEPENDENCIES
dvipng: yes [version 1.11]
ghostscript: yes [version 8.70]
latex: yes [version 3.141592]
pdftops: no
OPTIONAL PACKAGE DATA
dlls: no [skipping due to configuration]
============================================================================
* The following required packages can not be built:
* freetype
* Try installing freetype with `yum install
* freetype-devel` and pkg-config with `yum install
* pkg-config`
Cleaning up...
Removing source in /tmp/pip-req-build-qhS9W4
Removed
file:///usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0/src
from build tracker '/tmp/pip-req-tracker-EMXWiP'
Removed build tracker '/tmp/pip-req-tracker-EMXWiP'
Command "python setup.py egg_info" failed with error code 1 in
/tmp/pip-req-build-qhS9W4/
Exception information:
Traceback (most recent call last):
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/cli/base_command.py",
line 143, in main
status = self.run(options, args)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/commands/install.py",
line 318, in run
resolver.resolve(requirement_set)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
line 102, in resolve
self._resolve_one(requirement_set, req)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
line 256, in _resolve_one
abstract_dist = self._get_abstract_dist_for(req_to_install)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/resolve.py",
line 209, in _get_abstract_dist_for
self.require_hashes
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/operations/prepare.py",
line 298, in prepare_linked_requirement
abstract_dist.prep_for_dist(finder, self.build_isolation)
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/operations/prepare.py",
line 126, in prep_for_dist
self.req.run_egg_info()
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/req/req_install.py",
line 473, in run_egg_info
command_desc='python setup.py egg_info')
File
"/usr/local/sage-8.9/local/lib/python2.7/site-packages/pip/_internal/utils/misc.py",
line 705, in call_subprocess
% (command_desc, proc.returncode, cwd))
InstallationError: Command "python setup.py egg_info" failed with error code 1
in /tmp/pip-req-build-qhS9W4/
Error: installing with pip2 failed
********************************************************************************
Error installing matplotlib-2.2.4.p0
********************************************************************************
real 0m3.844s
user 0m2.335s
sys 0m1.265s
************************************************************************
Error installing package matplotlib-2.2.4.p0
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the log file
/usr/local/sage-8.9/logs/pkgs/matplotlib-2.2.4.p0.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0 and type
'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/usr/local/sage-8.9/local/var/tmp/sage/build/matplotlib-2.2.4.p0' &&
'/usr/local/sage-8.9/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
Found local metadata for r-3.6.1
Using cached file /usr/local/sage-8.9/upstream/R-3.6.1.tar.gz
r-3.6.1
====================================================
Setting up build directory for r-3.6.1
Finished extraction
Applying patches from ../patches...
Applying ../patches/autoconf_verb_dash.patch
patching file configure
Hunk #1 succeeded at 24879 with fuzz 2 (offset 42 lines).
Hunk #2 succeeded at 25236 (offset 43 lines).
Applying ../patches/cygwin_build_support.patch
patching file configure
Hunk #1 succeeded at 27468 (offset -255 lines).
Hunk #2 succeeded at 27710 (offset -286 lines).
Hunk #3 succeeded at 27723 (offset -286 lines).
Hunk #4 succeeded at 27736 (offset -286 lines).
patching file configure.ac
Hunk #1 succeeded at 1249 (offset -45 lines).
Hunk #2 succeeded at 1506 (offset -45 lines).
Hunk #3 succeeded at 1518 (offset -45 lines).
Hunk #4 succeeded at 1530 (offset -45 lines).
patching file src/library/tools/R/install.R
Hunk #1 succeeded at 1215 (offset 374 lines).
Applying ../patches/hardcoded_dirs.patch
patching file src/scripts/Makefile.in
Hunk #1 succeeded at 87 (offset -2 lines).
patching file src/scripts/R.sh.in
Applying ../patches/libcurl_https_support.patch
patching file configure
Hunk #1 succeeded at 42717 (offset 1648 lines).
Hunk #2 succeeded at 42726 (offset 1648 lines).
patching file m4/R.m4
Hunk #1 succeeded at 4108 (offset -97 lines).
Applying ../patches/link_all_shared_libs.patch
patching file etc/Makeconf.in
Hunk #1 succeeded at 158 with fuzz 2 (offset 8 lines).
Applying ../patches/m4_macro_bug.patch
patching file configure
Hunk #1 succeeded at 42317 (offset 1518 lines).
Hunk #2 succeeded at 42361 with fuzz 2 (offset 1518 lines).
patching file m4/R.m4
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Hunk #2 succeeded at 3049 with fuzz 2 (offset -163 lines).
Applying ../patches/rcmd_exec.patch
patching file src/scripts/Rcmd.in
****************************************************
Host system:
Linux algebra.math.yorku.ca 2.6.32-754.23.1.el6.centos.plus.x86_64 #1 SMP Thu
Sep 26 11:58:20 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=gcc
COLLECT_LTO_WRAPPER=/usr/local/sage-8.9/local/libexec/gcc/x86_64-pc-linux-gnu/7.4.0/lto-wrapper
Target: x86_64-pc-linux-gnu
Configured with: ../src/configure --prefix=/usr/local/sage-8.9/local
--with-local-prefix=/usr/local/sage-8.9/local
--with-gmp=/usr/local/sage-8.9/local --with-mpfr=/usr/local/sage-8.9/local
--with-mpc=/usr/local/sage-8.9/local --with-system-zlib --without-isl
--disable-multilib --disable-nls --disable-libitm
--enable-languages=c,c++,fortran
Thread model: posix
gcc version 7.4.0 (GCC)
****************************************************
Package 'r' is currently not installed
No legacy uninstaller found for 'r'; nothing to do
R_CONFIGURE_BLAS=--with-blas=-L/usr/local/sage-8.9/local/lib -lopenblas
R_CONFIGURE_LAPACK=--with-lapack=-L/usr/local/sage-8.9/local/lib -lopenblas
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checking whether mixed C/Fortran code can be run... yes
checking whether gfortran and gcc agree on int and double... yes
checking whether gfortran and gcc agree on double complex... yes
checking for gfortran option to support OpenMP... -fopenmp
checking whether g++ accepts -M for generating dependencies... yes
checking whether we can compute ObjC Make dependencies... no
checking if need -fno-optimize-sibling-calls for gfortran... yes
checking for xmkmf... no
checking whether g++ supports C++98 features with -std=gnu++98... yes
checking whether g++ supports C++11 features with -std=gnu++11... yes
checking whether g++ supports C++14 features with -std=gnu++14... yes
checking whether g++ supports C++17 features with -std=gnu++17... yes
checking for g++ -std=gnu++11 option to support OpenMP... -fopenmp
checking for option providing pthread_kill... none required
checking whether POSIX threads are supported... yes
checking for off_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether alloca is declared... yes
checking whether expm1 exists and is declared... yes
checking whether hypot exists and is declared... yes
checking whether log1p exists and is declared... yes
checking whether log1pl exists and is declared... yes
checking whether log2 exists and is declared... yes
checking whether log10 exists and is declared... yes
checking whether nearbyint exists and is declared... yes
checking whether nearbyintl exists and is declared... yes
checking whether powl exists and is declared... yes
checking whether rintl exists and is declared... yes
checking whether va_copy exists and is declared... yes
checking for isblank... yes
checking sunmath.h usability... no
checking sunmath.h presence... no
checking for sunmath.h... no
checking for cospi in -lsunmath... no
checking for atanpi... no
checking for atan2pi... no
checking for cospi... no
checking for exp10... yes
checking for pown... no
checking for sinpi... no
checking for tanpi... no
checking for __cospi... no
checking for __sinpi... no
checking for __tanpi... no
checking for fseeko... yes
checking for ftello... yes
checking for matherr... yes
checking whether fcntl exists and is declared... yes
checking whether getgrgid exists and is declared... yes
checking whether getpwuid exists and is declared... yes
checking whether kill exists and is declared... yes
checking whether sigaction exists and is declared... yes
checking whether sigaltstack exists and is declared... yes
checking whether sigemptyset exists and is declared... yes
checking whether fdopen exists and is declared... yes
checking whether popen exists and is declared... yes
checking whether getline exists and is declared... yes
checking whether select exists and is declared... yes
checking whether setenv exists and is declared... yes
checking whether unsetenv exists and is declared... yes
checking whether getrlimit exists and is declared... yes
checking whether setrlimit exists and is declared... yes
checking whether getrusage exists and is declared... yes
checking whether getpriority exists and is declared... yes
checking whether chmod exists and is declared... yes
checking whether mkfifo exists and is declared... yes
checking whether stat exists and is declared... yes
checking whether umask exists and is declared... yes
checking whether gettimeofday exists and is declared... yes
checking whether utimes exists and is declared... yes
checking whether times exists and is declared... yes
checking whether gmtime_r exists and is declared... yes
checking whether localtime_r exists and is declared... yes
checking whether nl_langinfo exists and is declared... yes
checking whether access exists and is declared... yes
checking whether chdir exists and is declared... yes
checking whether execv exists and is declared... yes
checking whether ftruncate exists and is declared... yes
checking whether getcwd exists and is declared... yes
checking whether geteuid exists and is declared... yes
checking whether getuid exists and is declared... yes
checking whether link exists and is declared... yes
checking whether readlink exists and is declared... yes
checking whether symlink exists and is declared... yes
checking whether sysconf exists and is declared... yes
checking whether sched_setaffinity exists and is declared... yes
checking whether sched_getaffinity exists and is declared... yes
checking whether utime exists and is declared... yes
checking whether utimensat exists and is declared... yes
checking for clock_gettime in -lrt... yes
checking whether clock_gettime exists and is declared... yes
checking whether timespec_get exists and is declared... no
checking for putenv... yes
checking whether putenv is declared... yes
checking for vasprintf... yes
checking whether vasprintf is declared... yes
checking for mempcpy... yes
checking for realpath... yes
checking whether realpath is declared... yes
checking whether glob exists and is declared... yes
checking for dladdr... yes
checking for dlsym... yes
checking whether dladdr is declared... yes
checking whether dlsym is declared... yes
checking whether RTLD_DEFAULT is declared... yes
checking whether RTLD_NEXT is declared... yes
checking thread.h usability... no
checking thread.h presence... no
checking for thread.h... no
checking whether thr_stksegment exists and is declared... no
checking for isnan... yes
checking whether isfinite is declared... yes
checking whether isnan is declared... yes
checking whether you have IEEE 754 floating-point arithmetic... yes
checking whether putenv("FOO") can unset an environment variable... yes
checking whether putenv("FOO=") can unset an environment variable... no
checking for nl_langinfo and CODESET... yes
checking for mkdtemp... yes
checking for strdup... yes
checking for strncasecmp... yes
checking whether mkdtemp is declared... yes
checking whether strdup is declared... yes
checking whether strncasecmp is declared... yes
checking for library containing connect... none required
checking for library containing gethostbyname... none required
checking for library containing xdr_string... none required
checking for working calloc... yes
checking for working isfinite... yes
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
checking for working sigaction... yes
checking whether mktime sets errno... no
checking whether mktime works correctly outside 1902-2037... yes
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for double complex... yes
checking whether C99 double complex is supported... yes
checking whether cabs exists and is declared... yes
checking whether carg exists and is declared... yes
checking whether cexp exists and is declared... yes
checking whether clog exists and is declared... yes
checking whether csqrt exists and is declared... yes
checking whether cpow exists and is declared... yes
checking whether ccos exists and is declared... yes
checking whether csin exists and is declared... yes
checking whether ctan exists and is declared... yes
checking whether cacos exists and is declared... yes
checking whether casin exists and is declared... yes
checking whether catan exists and is declared... yes
checking whether ccosh exists and is declared... yes
checking whether csinh exists and is declared... yes
checking whether ctanh exists and is declared... yes
checking for working ctanh... no
checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
checking for dgemm_ in -L/usr/local/sage-8.9/local/lib -lopenblas ... yes
checking whether double complex BLAS can be used... yes
checking whether the BLAS is complete... yes
checking for dpstrf_... yes
checking iconv.h usability... yes
checking iconv.h presence... yes
checking for iconv.h... yes
checking for iconv... yes
checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes
checking whether iconv accepts "CP1252"... yes
checking for iconvlist... no
checking for iconv... yes
checking for iconv declaration...
extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft,
char * *outbuf, size_t *outbytesleft);
checking wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
checking wctype.h usability... yes
checking wctype.h presence... yes
checking for wctype.h... yes
checking whether mbrtowc exists and is declared... yes
checking whether wcrtomb exists and is declared... yes
checking whether wcscoll exists and is declared... yes
checking whether wcsftime exists and is declared... yes
checking whether wcstod exists and is declared... yes
checking whether mbstowcs exists and is declared... yes
checking whether wcstombs exists and is declared... yes
checking whether wctrans exists and is declared... yes
checking whether iswblank exists and is declared... yes
checking whether wctype exists and is declared... yes
checking whether iswctype exists and is declared... yes
checking for wctrans_t... yes
checking for mbstate_t... yes
checking for ICU... no
checking for X... libraries , headers
checking for gethostbyname... yes
checking for connect... yes
checking for remove... yes
checking for shmat... yes
checking for IceConnectionNumber in -lICE... yes
checking X11/Intrinsic.h usability... yes
checking X11/Intrinsic.h presence... yes
checking for X11/Intrinsic.h... yes
checking for XtToolkitInitialize in -lXt... yes
using X11 ... yes
checking for KeySym... yes
checking X11/Xmu/Atoms.h usability... no
checking X11/Xmu/Atoms.h presence... no
checking for X11/Xmu/Atoms.h... no
checking whether pkg-config knows about cairo and pango... no
checking whether pkg-config knows about cairo... no
checking for tclConfig.sh... no
checking for tclConfig.sh in library (sub)directories... /usr/lib64/tclConfig.sh
checking for tkConfig.sh... no
checking for tkConfig.sh in library (sub)directories... /usr/lib64/tkConfig.sh
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
checking tk.h usability... yes
checking tk.h presence... yes
checking for tk.h... yes
checking whether compiling/linking Tcl/Tk code works... yes
checking for BSD networking... yes
checking rpc/types.h usability... yes
checking rpc/types.h presence... yes
checking for rpc/types.h... yes
checking for rpc/xdr.h... yes
checking for XDR support... yes
checking for inflateInit2_ in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.2.5... no
checking whether zlib support suffices... configure: error: zlib library and
headers are required
Configuring R without X11
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
loading site script './config.site'
loading build-specific script './config.site'
checking for pwd... /bin/pwd
checking whether builddir is srcdir... yes
checking whether ln -s works... yes
checking for ar... ar
checking for a BSD-compatible install... /usr/bin/install -c
checking for sed... /bin/sed
checking for which... /usr/bin/which
checking for less... /usr/bin/less
checking for gtar... /bin/gtar
checking for tex... /usr/bin/tex
checking for pdftex... /usr/bin/pdftex
checking for pdflatex... /usr/bin/pdflatex
checking for makeindex... /usr/bin/makeindex
checking for texi2any... no
configure: WARNING: you cannot build info or HTML versions of the R manuals
checking for texi2dvi... no
checking for kpsewhich... /usr/bin/kpsewhich
checking for latex inconsolata package... missing
configure: WARNING: neither inconsolata.sty nor zi4.sty found: PDF vignettes
and package manuals will not be rendered optimally
checking for unzip... /usr/bin/unzip
checking for zip... /usr/bin/zip
checking for gzip... /bin/gzip
checking for bzip2... /usr/bin/bzip2
checking for firefox... /usr/bin/firefox
using default browser ... /usr/bin/firefox
checking for acroread... no
checking for acroread4... no
checking for xdg-open... /usr/bin/xdg-open
checking for working aclocal... found
checking for working autoconf... found
checking for working autoheader... found
checking for bison... bison -y
checking for notangle... false
checking for realpath... false
checking for pkg-config... /usr/local/sage-8.9/local/bin/pkg-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking whether gcc needs -traditional... no
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking how to run the C preprocessor... gcc -E
looking for a modern Fortran compiler
checking whether we are using the GNU Fortran compiler... yes
checking whether gfortran accepts -g... yes
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking whether g++ -g -O2 can compile C++ code... yes
checking how to run the C++ preprocessor... g++ -E
checking whether __attribute__((visibility())) is supported... yes
checking whether gcc accepts -fvisibility... yes
checking whether g++ accepts -fvisibility... yes
checking whether gfortran accepts -fvisibility... yes
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking whether g++ can compile ObjC++... no
checking whether can compile ObjC++... no
checking for Objective C++ compiler... no working ObjC++ compiler found
checking how to print strings... printf
checking for a sed that does not truncate output... (cached) /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc... ld
checking if the linker (ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking the maximum length of command line arguments... 1966080
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu
format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format...
func_convert_file_noop
checking for ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking for gawk... gawk
checking command to parse /usr/bin/nm -B output from gcc object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... no
checking if : is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc supports -fno-rtti -fno-exceptions... no
checking for gcc option to produce PIC... -fPIC -DPIC
checking if gcc PIC flag -fPIC -DPIC works... yes
checking if gcc static flag -static works... no
checking if gcc supports -c -o file.o... yes
checking if gcc supports -c -o file.o... (cached) yes
checking whether the gcc linker (ld -m elf_x86_64) supports shared libraries...
yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -E
checking for ld used by g++... ld -m elf_x86_64
checking if the linker (ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ linker (ld -m elf_x86_64) supports shared libraries...
yes
checking for g++ option to produce PIC... -fPIC -DPIC
checking if g++ PIC flag -fPIC -DPIC works... yes
checking if g++ static flag -static works... no
checking if g++ supports -c -o file.o... yes
checking if g++ supports -c -o file.o... (cached) yes
checking whether the g++ linker (ld -m elf_x86_64) supports shared libraries...
yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking for gfortran option to produce PIC... -fPIC
checking if gfortran PIC flag -fPIC works... yes
checking if gfortran static flag -static works... no
checking if gfortran supports -c -o file.o... yes
checking if gfortran supports -c -o file.o... (cached) yes
checking whether the gfortran linker (ld -m elf_x86_64) supports shared
libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for cos in -lm... yes
checking for sin in -lm... yes
checking for dlopen in -ldl... yes
checking readline/history.h usability... yes
checking readline/history.h presence... yes
checking for readline/history.h... yes
checking readline/readline.h usability... yes
checking readline/readline.h presence... yes
checking for readline/readline.h... yes
checking for rl_callback_read_char in -lreadline... yes
checking for history_truncate_file... yes
checking for tilde_expand_word... yes
checking whether rl_callback_sigcleanup exists and is declared... no
checking whether rl_completion_matches exists and is declared... yes
checking whether rl_resize_terminal exists and is declared... yes
checking whether rl_sort_completion_matches exists and is declared... yes
checking for ANSI C header files... (cached) yes
checking for dirent.h that defines DIR... yes
checking for library containing opendir... none required
checking for sys/wait.h that is POSIX.1 compatible... yes
checking for dlfcn.h... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking glob.h usability... yes
checking glob.h presence... yes
checking for glob.h... yes
checking grp.h usability... yes
checking grp.h presence... yes
checking for grp.h... yes
checking pwd.h usability... yes
checking pwd.h presence... yes
checking for pwd.h... yes
checking sched.h usability... yes
checking sched.h presence... yes
checking for sched.h... yes
checking for strings.h... (cached) yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/select.h usability... yes
checking sys/select.h presence... yes
checking for sys/select.h... yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/stat.h... (cached) yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking sys/times.h usability... yes
checking sys/times.h presence... yes
checking for sys/times.h... yes
checking sys/utsname.h usability... yes
checking sys/utsname.h presence... yes
checking for sys/utsname.h... yes
checking for unistd.h... (cached) yes
checking utime.h usability... yes
checking utime.h presence... yes
checking for utime.h... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking elf.h usability... yes
checking elf.h presence... yes
checking for elf.h... yes
checking features.h usability... yes
checking features.h presence... yes
checking for features.h... yes
checking floatingpoint.h usability... no
checking floatingpoint.h presence... no
checking for floatingpoint.h... no
checking langinfo.h usability... yes
checking langinfo.h presence... yes
checking for langinfo.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking netinet/in.h usability... yes
checking netinet/in.h presence... yes
checking for netinet/in.h... yes
checking sys/param.h usability... yes
checking sys/param.h presence... yes
checking for sys/param.h... yes
checking stdalign.h usability... yes
checking stdalign.h presence... yes
checking for stdalign.h... yes
checking errno.h usability... yes
checking errno.h presence... yes
checking for errno.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking locale.h usability... yes
checking locale.h presence... yes
checking for locale.h... yes
checking stdarg.h usability... yes
checking stdarg.h presence... yes
checking for stdarg.h... yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking for stdint.h... (cached) yes
checking for string.h... (cached) yes
checking whether setjmp.h is POSIX.1 compatible... yes
checking whether sigsetjmp is declared... yes
checking whether siglongjmp is declared... yes
checking for GNU C library with version >= 2... yes
checking return type of signal handlers... void
checking for uint64_t... yes
checking for int64_t... yes
checking for int_fast64_t... yes
checking for pid_t... yes
checking for size_t... yes
checking whether SIZE_MAX is declared... yes
checking for blkcnt_t... yes
checking for type of socket length... socklen_t *
checking for stack_t... yes
checking for intptr_t... yes
checking for uintptr_t... yes
checking whether byte ordering is bigendian... no
checking for an ANSI C-conforming const... yes
checking for gcc option to accept ISO C99... none needed
checking for gcc option to accept ISO Standard C... (cached) none needed
checking for inline... inline
checking size of int... 4
checking size of long... 8
checking size of long long... 8
checking size of double... 8
checking size of size_t... 8
checking size of long double... 16
checking whether we can compute C Make dependencies... yes, using $(CC) -MM
checking whether gcc supports -c -o FILE.lo... yes
checking for gcc option to support OpenMP... -fopenmp
checking how to get verbose linking output from gfortran... -###
checking for Fortran libraries of gfortran... -L/usr/local/sage-8.9/local/lib
-L/usr/local/sage-8.9/local/lib/../lib
-L/usr/local/sage-8.9/local/lib/gcc/x86_64-pc-linux-gnu/7.4.0
-L/usr/local/sage-8.9/local/lib/gcc/x86_64-pc-linux-gnu/7.4.0/../../../../lib
-L/lib/../lib -L/usr/lib/../lib
-L/usr/local/sage-8.9/local/lib/gcc/x86_64-pc-linux-gnu/7.4.0/../../..
-lgfortran -lm -lquadmath
checking how to get verbose linking output from gcc... -###
checking for C libraries of gcc... -L/usr/local/sage-8.9/local/lib
-L/usr/local/sage-8.9/local/lib/../lib
-L/usr/local/sage-8.9/local/lib/gcc/x86_64-pc-linux-gnu/7.4.0
-L/usr/local/sage-8.9/local/lib/gcc/x86_64-pc-linux-gnu/7.4.0/../../../../lib
-L/lib/../lib -L/usr/lib/../lib
-L/usr/local/sage-8.9/local/lib/gcc/x86_64-pc-linux-gnu/7.4.0/../../.. -lgcc_s
checking for dummy main to link with Fortran libraries... none
checking for Fortran name-mangling scheme... lower case, underscore, no extra
underscore
checking whether gfortran appends underscores to external names... yes
checking whether gfortran appends extra underscores to external names... no
checking whether mixed C/Fortran code can be run... yes
checking whether gfortran and gcc agree on int and double... yes
checking whether gfortran and gcc agree on double complex... yes
checking for gfortran option to support OpenMP... -fopenmp
checking whether g++ accepts -M for generating dependencies... yes
checking whether we can compute ObjC Make dependencies... no
checking if need -fno-optimize-sibling-calls for gfortran... yes
checking for xmkmf... no
checking whether g++ supports C++98 features with -std=gnu++98... yes
checking whether g++ supports C++11 features with -std=gnu++11... yes
checking whether g++ supports C++14 features with -std=gnu++14... yes
checking whether g++ supports C++17 features with -std=gnu++17... yes
checking for g++ -std=gnu++11 option to support OpenMP... -fopenmp
checking for option providing pthread_kill... none required
checking whether POSIX threads are supported... yes
checking for off_t... yes
checking for working alloca.h... yes
checking for alloca... yes
checking whether alloca is declared... yes
checking whether expm1 exists and is declared... yes
checking whether hypot exists and is declared... yes
checking whether log1p exists and is declared... yes
checking whether log1pl exists and is declared... yes
checking whether log2 exists and is declared... yes
checking whether log10 exists and is declared... yes
checking whether nearbyint exists and is declared... yes
checking whether nearbyintl exists and is declared... yes
checking whether powl exists and is declared... yes
checking whether rintl exists and is declared... yes
checking whether va_copy exists and is declared... yes
checking for isblank... yes
checking sunmath.h usability... no
checking sunmath.h presence... no
checking for sunmath.h... no
checking for cospi in -lsunmath... no
checking for atanpi... no
checking for atan2pi... no
checking for cospi... no
checking for exp10... yes
checking for pown... no
checking for sinpi... no
checking for tanpi... no
checking for __cospi... no
checking for __sinpi... no
checking for __tanpi... no
checking for fseeko... yes
checking for ftello... yes
checking for matherr... yes
checking whether fcntl exists and is declared... yes
checking whether getgrgid exists and is declared... yes
checking whether getpwuid exists and is declared... yes
checking whether kill exists and is declared... yes
checking whether sigaction exists and is declared... yes
checking whether sigaltstack exists and is declared... yes
checking whether sigemptyset exists and is declared... yes
checking whether fdopen exists and is declared... yes
checking whether popen exists and is declared... yes
checking whether getline exists and is declared... yes
checking whether select exists and is declared... yes
checking whether setenv exists and is declared... yes
checking whether unsetenv exists and is declared... yes
checking whether getrlimit exists and is declared... yes
checking whether setrlimit exists and is declared... yes
checking whether getrusage exists and is declared... yes
checking whether getpriority exists and is declared... yes
checking whether chmod exists and is declared... yes
checking whether mkfifo exists and is declared... yes
checking whether stat exists and is declared... yes
checking whether umask exists and is declared... yes
checking whether gettimeofday exists and is declared... yes
checking whether utimes exists and is declared... yes
checking whether times exists and is declared... yes
checking whether gmtime_r exists and is declared... yes
checking whether localtime_r exists and is declared... yes
checking whether nl_langinfo exists and is declared... yes
checking whether access exists and is declared... yes
checking whether chdir exists and is declared... yes
checking whether execv exists and is declared... yes
checking whether ftruncate exists and is declared... yes
checking whether getcwd exists and is declared... yes
checking whether geteuid exists and is declared... yes
checking whether getuid exists and is declared... yes
checking whether link exists and is declared... yes
checking whether readlink exists and is declared... yes
checking whether symlink exists and is declared... yes
checking whether sysconf exists and is declared... yes
checking whether sched_setaffinity exists and is declared... yes
checking whether sched_getaffinity exists and is declared... yes
checking whether utime exists and is declared... yes
checking whether utimensat exists and is declared... yes
checking for clock_gettime in -lrt... yes
checking whether clock_gettime exists and is declared... yes
checking whether timespec_get exists and is declared... no
checking for putenv... yes
checking whether putenv is declared... yes
checking for vasprintf... yes
checking whether vasprintf is declared... yes
checking for mempcpy... yes
checking for realpath... yes
checking whether realpath is declared... yes
checking whether glob exists and is declared... yes
checking for dladdr... yes
checking for dlsym... yes
checking whether dladdr is declared... yes
checking whether dlsym is declared... yes
checking whether RTLD_DEFAULT is declared... yes
checking whether RTLD_NEXT is declared... yes
checking thread.h usability... no
checking thread.h presence... no
checking for thread.h... no
checking whether thr_stksegment exists and is declared... no
checking for isnan... yes
checking whether isfinite is declared... yes
checking whether isnan is declared... yes
checking whether you have IEEE 754 floating-point arithmetic... yes
checking whether putenv("FOO") can unset an environment variable... yes
checking whether putenv("FOO=") can unset an environment variable... no
checking for nl_langinfo and CODESET... yes
checking for mkdtemp... yes
checking for strdup... yes
checking for strncasecmp... yes
checking whether mkdtemp is declared... yes
checking whether strdup is declared... yes
checking whether strncasecmp is declared... yes
checking for library containing connect... none required
checking for library containing gethostbyname... none required
checking for library containing xdr_string... none required
checking for working calloc... yes
checking for working isfinite... yes
checking for working log1p... yes
checking whether ftell works correctly on files opened for append... yes
checking for working sigaction... yes
checking whether mktime sets errno... no
checking whether mktime works correctly outside 1902-2037... yes
checking complex.h usability... yes
checking complex.h presence... yes
checking for complex.h... yes
checking for double complex... yes
checking whether C99 double complex is supported... yes
checking whether cabs exists and is declared... yes
checking whether carg exists and is declared... yes
checking whether cexp exists and is declared... yes
checking whether clog exists and is declared... yes
checking whether csqrt exists and is declared... yes
checking whether cpow exists and is declared... yes
checking whether ccos exists and is declared... yes
checking whether csin exists and is declared... yes
checking whether ctan exists and is declared... yes
checking whether cacos exists and is declared... yes
checking whether casin exists and is declared... yes
checking whether catan exists and is declared... yes
checking whether ccosh exists and is declared... yes
checking whether csinh exists and is declared... yes
checking whether ctanh exists and is declared... yes
checking for working ctanh... no
checking whether 'struct tm' includes tm_zone... yes
checking whether 'struct tm' includes tm_gmtoff... yes
checking for dgemm_ in -L/usr/local/sage-8.9/local/lib -lopenblas ... yes
checking whether double complex BLAS can be used... yes
checking whether the BLAS is complete... yes
checking for dpstrf_... yes
checking iconv.h usability... yes
checking iconv.h presence... yes
checking for iconv.h... yes
checking for iconv... yes
checking whether iconv accepts "UTF-8", "latin1", "ASCII" and "UCS-*"... yes
checking whether iconv accepts "CP1252"... yes
checking for iconvlist... no
checking for iconv... yes
checking for iconv declaration...
extern size_t iconv (iconv_t cd, char * *inbuf, size_t *inbytesleft,
char * *outbuf, size_t *outbytesleft);
checking wchar.h usability... yes
checking wchar.h presence... yes
checking for wchar.h... yes
checking wctype.h usability... yes
checking wctype.h presence... yes
checking for wctype.h... yes
checking whether mbrtowc exists and is declared... yes
checking whether wcrtomb exists and is declared... yes
checking whether wcscoll exists and is declared... yes
checking whether wcsftime exists and is declared... yes
checking whether wcstod exists and is declared... yes
checking whether mbstowcs exists and is declared... yes
checking whether wcstombs exists and is declared... yes
checking whether wctrans exists and is declared... yes
checking whether iswblank exists and is declared... yes
checking whether wctype exists and is declared... yes
checking whether iswctype exists and is declared... yes
checking for wctrans_t... yes
checking for mbstate_t... yes
checking for ICU... no
checking for X... disabled
using X11 ... no
checking whether pkg-config knows about cairo and pango... no
checking whether pkg-config knows about cairo... no
checking for tclConfig.sh... no
checking for tclConfig.sh in library (sub)directories... /usr/lib64/tclConfig.sh
checking for tkConfig.sh... no
checking for tkConfig.sh in library (sub)directories... /usr/lib64/tkConfig.sh
checking tcl.h usability... yes
checking tcl.h presence... yes
checking for tcl.h... yes
checking tk.h usability... yes
checking tk.h presence... yes
checking for tk.h... yes
checking whether compiling/linking Tcl/Tk code works... yes
checking for BSD networking... yes
checking rpc/types.h usability... yes
checking rpc/types.h presence... yes
checking for rpc/types.h... yes
checking for rpc/xdr.h... yes
checking for XDR support... yes
checking for inflateInit2_ in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.2.5... no
checking whether zlib support suffices... configure: error: zlib library and
headers are required
Error configuring R.
real 0m50.807s
user 0m26.370s
sys 0m19.367s
************************************************************************
Error installing package r-3.6.1
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the log file
/usr/local/sage-8.9/logs/pkgs/r-3.6.1.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/usr/local/sage-8.9/local/var/tmp/sage/build/r-3.6.1 and type 'make' or
whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd '/usr/local/sage-8.9/local/var/tmp/sage/build/r-3.6.1' &&
'/usr/local/sage-8.9/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
